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With this program you can combine multiple ChIP-seq peaks lists (i.e.,ChIPseeqer outputs), for example setA, setB, setC, setD, etc, into a merged list of peak intervals. This is the union of all peak files, (setA ∪ setB ∪ setC ∪ setD)

The script uses Compare Intervals to output a textfile containing the overlapping interval of the peaks among all peakfiles given as input.

This analysis requires that ChIPseeqer has run multiple times, one for each ChIPseq dataset, and one peak file per dataset is created.

The script takes as input a file (coreTFFile) with the names of peak files (i.e., typical output of ChIPseeqer) followed by a label.

Example of the coreTFFile.

Bcl6Ly1_peaks.txt	Bcl6Ly1
BCOR_peaks.txt	        BCOR
CTCF_peaks.txt	        CTCF
h3k4me1_peaks.txt	h3k4me1
h3k4me3_peaks.txt	h3k4me3

1. To run the program, type the command:

CompareIntervalsMergedMultiEncode --coreTFFile=all_peak_files.txt --outfile=H1_Esc_CREs.txt

Available options are:

--coreTFFile FILE   file containing the names and labels of the peak files
--outfile FILE     output file
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